From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems

In the last decade, the CRISPR-Cas technology has gained widespread popularity in different fields from genome editing and detecting specific DNA/RNA sequences to gene expression control. At the heart of this technology is the ability of CRISPR-Cas complexes to be programmed for targeting particular DNA loci, even when using catalytically inactive dCas-proteins. The repertoire of naturally derived and engineered dCas-proteins including fusion proteins presents a promising toolbox that can be used to construct functional synthetic genetic circuits. Rational genetic circuit design, apart from having practical relevance, is an important step towards a deeper quantitative understanding of the basic principles governing gene expression regulation and functioning of living organisms. In this minireview, we provide a succinct overview of the application of CRISPR-dCas-based systems in the emerging field of synthetic genetic circuit design. We discuss the diversity of dCas-based tools, their properties, and their application in different types of genetic circuits and outline challenges and further research directions in the field

Exact analytical solution of the problem of current-carrying states of the Josephson junction in external magnetic fields

The classical problem of the Josephson junction of arbitrary length W in the presence of externally applied magnetic fields (H) and transport currents (J) is reconsidered from the point of view of stability theory. In particular, we derive the complete infinite set of exact analytical solutions for the phase difference that describe the current-carrying states of the junction with arbitrary W and an arbitrary mode of the injection of J. These solutions are parameterized by two natural parameters: the constants of integration. The boundaries of their stability regions in the parametric plane are determined by a corresponding infinite set of exact functional equations. Being mapped to the physical plane (H,J), these boundaries yield the dependence of the critical transport current Jc on H. Contrary to a wide-spread belief, the exact analytical dependence Jc=Jc(H) proves to be multivalued even for arbitrarily small W. What is more, the exact solution reveals the existence of unquantized Josephson vortices carrying fractional flux and located near one of the junction edges, provided that J is sufficiently close to Jc for certain finite values of H. This conclusion (as well as other exact analytical results) is illustrated by a graphical analysis of typical cases.Comment: 21 pages, 9 figures, to be published in Phys. Rev.

Local hyperactivation of L-type Ca2+ channels increases spontaneous Ca2+ release activity and cellular hypertrophy in right ventricular myocytes from heart failure rats

Right ventricle (RV) dysfunction is an independent predictor of patient survival in heart failure (HF). However, the mechanisms of RV progression towards failing are not well understood. We studied cellular mechanisms of RV remodelling in a rat model of left ventricle myocardial infarction (MI)-caused HF. RV myocytes from HF rats show significant cellular hypertrophy accompanied with a disruption of transverse-axial tubular network and surface flattening. Functionally these cells exhibit higher contractility with lower Ca2+ transients. The structural changes in HF RV myocytes correlate with more frequent spontaneous Ca2+ release activity than in control RV myocytes. This is accompanied by hyperactivated L-type Ca2+ channels (LTCCs) located specifically in the T-tubules of HF RV myocytes. The increased open probability of tubular LTCCs and Ca2+ sparks activation is linked to protein kinase A-mediated channel phosphorylation that occurs locally in T-tubules. Thus, our approach revealed that alterations in RV myocytes in heart failure are specifically localized in microdomains. Our findings may indicate the development of compensatory, though potentially arrhythmogenic, RV remodelling in the setting of LV failure. These data will foster better understanding of mechanisms of heart failure and it could promote an optimized treatment of patients

Static Solitons of the Sine-Gordon Equation and Equilibrium Vortex Structure in Josephson Junctions

The problem of vortex structure in a single Josephson junction in an external magnetic field, in the absence of transport currents, is reconsidered from a new mathematical point of view. In particular, we derive a complete set of exact analytical solutions representing all the stationary points (minima and saddle-points) of the relevant Gibbs free-energy functional. The type of these solutions is determined by explicit evaluation of the second variation of the Gibbs free-energy functional. The stable (physical) solutions minimizing the Gibbs free-energy functional form an infinite set and are labelled by a topological number Nv=0,1,2,... Mathematically, they can be interpreted as nontrivial ''vacuum'' (Nv=0) and static topological solitons (Nv=1,2,...) of the sine-Gordon equation for the phase difference in a finite spatial interval: solutions of this kind were not considered in previous literature. Physically, they represent the Meissner state (Nv=0) and Josephson vortices (Nv=1,2,...). Major properties of the new physical solutions are thoroughly discussed. An exact, closed-form analytical expression for the Gibbs free energy is derived and analyzed numerically. Unstable (saddle-point) solutions are also classified and discussed.Comment: 17 pages, 4 Postscript figure

Composition and morphology of metal microparticles in paleozoic sediments of caspian depression

© Research India Publications 2015. Using the microprobe analysis 18 samples of metallic micro-particles were studied (spheres, plates, coils, wire) from Paleozoic deposits of the Caspian basin. The morphology of the microparticles and their chemical composition showed that the microparticles have different origins. The formation of spiral and wire type forms is associated with volcanic activity, and magnetite microspheres were formed in the Earth atmosphere during the flight and meteorite ablation. It is determined that Mn (0.8-2%), rarely Cr is uniformly distributed in magnetite microspheres. In the interstices of magnetite tablets the releases of native nickel, nickel oxides, the awaruite of Ni3Fe are met rarely. Among the spiral formations the intermetallic compositions of Fe-Cr-Mn and Fe-Cr-Ni are met and the mechanism of their formation in the development of subvolcanic chamber is proposed. The diagrams lg (Cr/Ni) - lg (Cr/Mn) and lg (Fe/Cr) - lg (Fe/Ni) allow to reveal the geochemical differences of metallic microparticles of volcanic and cosmic origin. The metallic microparticles discovered in sedimentary rocks, may be an additional tool for regional parallelization of multipartite cuts, may lead to the revision of biotic process models, the assessment of terrestrial and cosmic processes impact on them, help in the search for hydrocarbon deposits and stratified deposits of solid minerals

Cosmic microspheres in the Carboniferous deposits of the Usolka section (Urals foredeep)

© 2017Magnetite microspheres from the Carboniferous deposits of the Usolka reference section were studied by probe microanalysis, with comparison of the distributions of chemical elements and microspheres. The presence of microspheres in sedimentary strata is considered to be an additional factor for stratigraphic correlation between sedimentary sections. The microspheres are shown to be of cosmic nature. The Late Paleozoic paleoclimatic changes (extreme cooling) and biotic crises were caused by the periodical Solar System motion in the Galaxy, cosmic-dust fallout, and meteorite bombardments of the Earth

Local hyperactivation of L-type Ca2+ channels increases spontaneous Ca2+ release activity and cellular hypertrophy in right ventricular myocytes from heart failure rats

Right ventricle (RV) dysfunction is an independent predictor of patient survival in heart failure (HF). However, the mechanisms of RV progression towards failing are not well understood. We studied cellular mechanisms of RV remodelling in a rat model of left ventricle myocardial infarction (MI)-caused HF. RV myocytes from HF rats show significant cellular hypertrophy accompanied with a disruption of transverse-axial tubular network and surface flattening. Functionally these cells exhibit higher contractility with lower Ca2+ transients. The structural changes in HF RV myocytes correlate with more frequent spontaneous Ca2+ release activity than in control RV myocytes. This is accompanied by hyperactivated L-type Ca2+ channels (LTCCs) located specifically in the T-tubules of HF RV myocytes. The increased open probability of tubular LTCCs and Ca2+ sparks activation is linked to protein kinase A-mediated channel phosphorylation that occurs locally in T-tubules. Thus, our approach revealed that alterations in RV myocytes in heart failure are specifically localized in microdomains. Our findings may indicate the development of compensatory, though potentially arrhythmogenic, RV remodelling in the setting of LV failure. These data will foster better understanding of mechanisms of heart failure and it could promote an optimized treatment of patients

Universal Crossover between Efros-Shklovskii and Mott Variable-Range-Hopping Regimes

A universal scaling function, describing the crossover between the Mott and the Efros-Shklovskii hopping regimes, is derived, using the percolation picture of transport in strongly localized systems. This function is agrees very well with experimental data. Quantitative comparison with experiment allows for the possible determination of the role played by polarons in the transport.Comment: 7 pages + 1 figure, Revte

Improvement of Protective Oxide Layers Formed by Highfrequency Plasma Electrolytic Oxidation on Mg-RE Alloy with LPSO-Phase

Received: 17.04.23. Revised: 17.05.23. Accepted: 23.05.23. Available online: 29.05.23.PEO of Mg-RE (LPSO) alloy allows improving its corrosion behaviour and surface mechanical properties.Increase of pulse frequency under PEO allows decreasing the porosity and heterogeneity of the oxide layers.The best corrosion resistance and adhesive strength demonstrate the oxide layer obtained in aluminate electrolyte under high-frequency PEO.Oxide layers on Mg97Y2Zn1 magnesium alloy with strengthening LPSO-phase were formed by plasma electrolytic oxidation (PEO) in bipolar mode with frequency variation of forming current pulses (50 and 500 Hz) and addition of sodium aluminate or sodium silicate to alkali phosphate fluoride electrolyte. Microstructure, chemical and phase composition, corrosion and mechanical properties of the oxide layers formed were investigated. With increasing current frequency for both electrolytes, an increase in homogeneity of the oxide layers structure and a decrease in their porosity and fracturing at constant thickness were recorded. The oxide layers formed at 500 Hz even with some decrease in hardness have better adhesive strength and 2 orders of magnitude higher short-term corrosion resistance values. PEO of Mg-alloy with LPSO-phase in the electrolyte with addition of sodium aluminate in combination with increased pulse frequency (500 Hz) allows forming the best-quality uniform oxide layer with high hardness, adhesive strength and corrosion resistance properties. The use of electrolyte with addition of sodium silicate reduced the adhesive strength by 1.5 times and brought down the long-term corrosion resistance of oxide layers by an order of magnitude, as compared with the electrolyte with sodium aluminate. The reason for a significant improvement in the complex of protective properties of the oxide layers with an increase in the current pulse frequency is supposed to be a decrease in the power and duration of individual microarc discharges with simultaneous increase in their number per unit oxidized area.Financial support is provided by the Russian Science Foundation (grant No. 20-79-10262), https://rscf.ru/project/20-79-10262/

Improvement of protective oxide layers formed by high-frequency plasma electrolytic oxidation on Mg-RE alloy with LPSO-phase

Oxide layers on Mg97Y2Zn1 magnesium alloy with strengthening LPSO-phase were formed by plasma electrolytic oxidation (PEO) in bipolar mode with frequency variation of forming current pulses (50 and 500 Hz) and addition of sodium aluminate or sodium silicate to alkali phosphate fluoride electrolyte. Microstructure, chemical and phase composition, corrosion and mechanical properties of the oxide layers formed were investigated. With increasing current frequency for both electrolytes, an increase in homogeneity of the oxide layers structure and a decrease in their porosity and fracturing at constant thickness were recorded. The oxide layers formed at 500 Hz even with some decrease in hardness have better adhesive strength and 2 orders of magnitude higher short-term corrosion resistance values. PEO of Mg-alloy with LPSO-phase in the electrolyte with addition of sodium aluminate in combination with increased pulse frequency (500 Hz) allows forming the best-quality uniform oxide layer with high hardness, adhesive strength and corrosion resistance properties. The use of electrolyte with addition of sodium silicate reduced the adhesive strength by 1.5 times and brought down the long-term corrosion resistance of oxide layers by an order of magnitude, as compared with the electrolyte with sodium aluminate. The reason for a significant improvement in the complex of protective properties of the oxide layers with an increase in the current pulse frequency is supposed to be a decrease in the power and duration of individual microarc discharges with simultaneous increase in their number per unit oxidized area